Package picard.sam
Interface PrimaryAlignmentSelectionStrategy
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- All Known Implementing Classes:
BestEndMapqPrimaryAlignmentStrategy
,BestMapqPrimaryAlignmentSelectionStrategy
,EarliestFragmentPrimaryAlignmentSelectionStrategy
,MostDistantPrimaryAlignmentSelectionStrategy
public interface PrimaryAlignmentSelectionStrategy
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate. Any pre-existing primary designation is ignored, so if the aligner has selected an appropriate primary alignment, this class should not be called.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert)
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
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